BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716926.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 1,781,454 number of mapped reads = 1,649,770 (92.61%) number of supplementary alignments = 8,394 (0.47%) number of secondary alignments = 0 number of mapped bases = 96,171,225 bp number of sequenced bases = 96,145,676 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 57,891 duplication rate = 2.62% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.884 >>>>>>> ACTG content number of A's = 24,056,448 bp (25.02%) number of C's = 19,580,834 bp (20.37%) number of T's = 29,296,911 bp (30.47%) number of G's = 23,208,810 bp (24.14%) number of N's = 2,673 bp (0%) GC percentage = 44.51% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 460,821 number of insertions = 6,575 mapped reads with insertion percentage = 0.4% number of deletions = 16,148 mapped reads with deletion percentage = 0.97% homopolymer indels = 42.86% >>>>>>> Coverage mean coverageData = 0.0311X std coverageData = 0.274X There is a 2.78% of reference with a coverageData >= 1X There is a 0.24% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 11601093 0.04654388804912948 0.47677514617544015 chr2 243199373 8309730 0.03416838578773803 0.34953800755228753 chr3 198022430 6747169 0.03407275125348174 0.20590309683261687 chr4 191154276 4521333 0.02365279550429727 0.17517832022932062 chr5 180915260 4265428 0.023576938728109502 0.17156200356849907 chr6 171115067 7349867 0.04295277516386094 0.298499574975737 chr7 159138663 5536635 0.03479126251048119 0.33817888324858947 chr8 146364022 6983072 0.04771030410738508 0.2679786380101425 chr9 141213431 4020070 0.028468042816692133 0.2385812219040269 chr10 135534747 4883160 0.03602884210939649 0.31630227512161835 chr11 135006516 3166544 0.023454749398910495 0.21662918536170603 chr12 133851895 4281622 0.03198775781246877 0.2026810591234444 chr13 115169878 2240999 0.019458204166891625 0.1538388196721475 chr14 107349540 3088673 0.02877211211151906 0.20202985213700733 chr15 102531392 2886391 0.02815129048477173 0.18387479067419765 chr16 90354753 2036606 0.022540109207093952 0.18531586050868448 chr17 81195210 2195847 0.027044046071190653 0.18546523666577394 chr18 78077248 1911626 0.024483777911844435 0.416464243822248 chr19 59128983 2042734 0.034547084971848746 0.34218855942683635 chr20 63025520 1651905 0.02621009711621578 0.17863159811101773 chr21 48129895 888072 0.018451567367849028 0.16718256069882112 chr22 51304566 1188709 0.023169653164983404 0.1674550997515624 chrMT 16571 15349 0.9262567135356949 1.117165746097733 chrX 155270560 4140939 0.02666918313426576 0.20514386165814869 chrY 59373566 217652 0.003665806429750236 0.08992146576010382